Examples with SEDMLExporter org.vcell.sedml.SEDMLExporter used on opensource projects

Example 1 with SEDMLExporter

use of org.vcell.sedml.SEDMLExporter in project vcell by virtualcell.

the class OmexExtensionFilter method writeBioModel.

@Override
public void writeBioModel(DocumentManager documentManager, BioModel bioModel, File exportFile, SimulationContext ignored) throws Exception {
    String resultString;
    // export the entire biomodel to a SEDML file (all supported applications)
    int sedmlLevel = 1;
    int sedmlVersion = 2;
    String sPath = FileUtils.getFullPathNoEndSeparator(exportFile.getAbsolutePath());
    String sFile = FileUtils.getBaseName(exportFile.getAbsolutePath());
    String sExt = FileUtils.getExtension(exportFile.getAbsolutePath());
    SEDMLExporter sedmlExporter = null;
    if (bioModel != null) {
        Object[] options = { "VCML", "SBML" };
        int choice = // parent component
        JOptionPane.showOptionDialog(// parent component
        null, // message,
        "VCML or SBML?", // title
        "Choose an option", // optionType
        JOptionPane.YES_NO_OPTION, // messageType
        JOptionPane.QUESTION_MESSAGE, // Icon
        null, options, // initialValue
        "VCML");
        boolean bForceVCML = choice == 0 ? true : false;
        sedmlExporter = new SEDMLExporter(bioModel, sedmlLevel, sedmlVersion, null);
        resultString = sedmlExporter.getSEDMLFile(sPath, sFile, bForceVCML, false, true);
        // convert biomodel to vcml and save to file.
        String vcmlString = XmlHelper.bioModelToXML(bioModel);
        String vcmlFileName = Paths.get(sPath, sFile + ".vcml").toString();
        File vcmlFile = new File(vcmlFileName);
        XmlUtil.writeXMLStringToFile(vcmlString, vcmlFile.getAbsolutePath(), true);
    } else {
        throw new RuntimeException("unsupported Document Type " + Objects.requireNonNull(bioModel).getClass().getName() + " for SedML export");
    }
    if (sExt.equals("omex")) {
        doSpecificWork(sedmlExporter, resultString, sPath, sFile);
        return;
    } else {
        XmlUtil.writeXMLStringToFile(resultString, exportFile.getAbsolutePath(), true);
    }
}

Example 2 with SEDMLExporter

use of org.vcell.sedml.SEDMLExporter in project vcell by virtualcell.

the class SedmlExtensionFilter method writeBioModel.

@Override
public void writeBioModel(DocumentManager documentManager, BioModel bioModel, File exportFile, SimulationContext ignored) throws Exception {
    String resultString;
    // export the entire biomodel to a SEDML file (for now, only non-spatial,non-stochastic applns)
    int sedmlLevel = 1;
    int sedmlVersion = 1;
    String sPath = FileUtils.getFullPathNoEndSeparator(exportFile.getAbsolutePath());
    String sFile = FileUtils.getBaseName(exportFile.getAbsolutePath());
    String sExt = FileUtils.getExtension(exportFile.getAbsolutePath());
    SEDMLExporter sedmlExporter = null;
    if (bioModel != null) {
        Object[] options = { "VCML", "SBML" };
        int choice = // parent component
        JOptionPane.showOptionDialog(// parent component
        null, // message,
        "VCML or SBML?", // title
        "Choose an option", // optionType
        JOptionPane.YES_NO_OPTION, // messageType
        JOptionPane.QUESTION_MESSAGE, // Icon
        null, options, // initialValue
        "VCML");
        boolean bForceVCML = choice == 0 ? true : false;
        sedmlExporter = new SEDMLExporter(bioModel, sedmlLevel, sedmlVersion, null);
        resultString = sedmlExporter.getSEDMLFile(sPath, sFile, bForceVCML, false, false);
    } else {
        throw new RuntimeException("unsupported Document Type " + Objects.requireNonNull(bioModel).getClass().getName() + " for SedML export");
    }
    if (sExt.equals("sedml")) {
        doSpecificWork(sedmlExporter, resultString, sPath, sFile);
        return;
    } else {
        XmlUtil.writeXMLStringToFile(resultString, exportFile.getAbsolutePath(), true);
    }
}

Example 3 with SEDMLExporter

use of org.vcell.sedml.SEDMLExporter in project vcell by virtualcell.

the class VcmlOmexConverter method vcmlToOmexConversion.

public static boolean vcmlToOmexConversion(String outputBaseDir) throws XmlParseException, IOException, DataAccessException, SQLException {
    // Get VCML file path from -i flag
    int sedmlLevel = 1;
    int sedmlVersion = 2;
    String inputVcmlFile = cliHandler.getInputFilePath();
    // Get directory file path from -o flag
    String outputDir = cliHandler.getOutputDirPath();
    // get VCML name from VCML path
    // String vcmlName = inputVcmlFile.split(File.separator, 10)[inputVcmlFile.split(File.separator, 10).length - 1].split("\\.", 5)[0];
    // platform independent, strips extension too
    String vcmlName = FilenameUtils.getBaseName(inputVcmlFile);
    File vcmlFilePath = new File(inputVcmlFile);
    // Create biomodel
    BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(vcmlFilePath));
    bioModel.refreshDependencies();
    int numSimulations = bioModel.getNumSimulations();
    if (outputBaseDir != null && numSimulations == 0) {
        CLIStandalone.writeSimErrorList(outputBaseDir, vcmlName + " has no simulations.");
        return false;
    }
    // we extract the simulations with field data from the list of simulations since they are not supported
    List<Simulation> simulationsToRemove = new ArrayList<>();
    for (Simulation simulation : bioModel.getSimulations()) {
        boolean bFieldDataFound = false;
        Enumeration<Variable> variables = simulation.getMathDescription().getVariables();
        while (variables.hasMoreElements()) {
            Variable var = variables.nextElement();
            Expression exp = var.getExpression();
            FieldFunctionArguments[] ffas = FieldUtilities.getFieldFunctionArguments(exp);
            if (ffas != null && ffas.length > 0) {
                bFieldDataFound = true;
                // we are done with this simulation if we know it has at least one variable with a field data in its expression
                break;
            }
        }
        if (bFieldDataFound) {
            simulationsToRemove.add(simulation);
            CLIStandalone.writeSimErrorList(outputBaseDir, vcmlName + " excluded: FieldData not supported at this time.");
            SolverDescription solverDescription = simulation.getSolverTaskDescription().getSolverDescription();
            String solverName = solverDescription.getShortDisplayLabel();
            CLIStandalone.writeSimErrorList(outputBaseDir, "   " + solverName);
        }
    }
    for (Simulation simulation : simulationsToRemove) {
        try {
            bioModel.removeSimulation(simulation);
        } catch (PropertyVetoException e) {
            System.out.println("Failed to remove simulation with field data");
            e.printStackTrace();
        }
    }
    // we replace the obsolete solver with the fully supported equivalent
    for (Simulation simulation : bioModel.getSimulations()) {
        if (simulation.getSolverTaskDescription().getSolverDescription().equals(SolverDescription.FiniteVolume)) {
            try {
                simulation.getSolverTaskDescription().setSolverDescription(SolverDescription.SundialsPDE);
            } catch (PropertyVetoException e) {
                System.out.println("Failed to replace obsolete solver");
                e.printStackTrace();
            }
        }
    }
    // NOTE: SEDML exporter exports both SEDML as well as required SBML
    List<Simulation> simsToExport = null;
    Set<String> solverNames = new LinkedHashSet<>();
    if (bHasDataOnly) {
        // make list of simulations to export with only sims that have data on the server
        simsToExport = new ArrayList<Simulation>();
        for (Simulation simulation : bioModel.getSimulations()) {
            SolverDescription solverDescription = simulation.getSolverTaskDescription().getSolverDescription();
            String solverName = solverDescription.getShortDisplayLabel();
            solverNames.add(solverName);
            // check server status
            KeyValue parentKey = simulation.getSimulationVersion().getParentSimulationReference();
            SimulationJobStatusPersistent[] statuses = adminDbTopLevel.getSimulationJobStatusArray(parentKey == null ? simulation.getKey() : parentKey, false);
            if (statuses == null)
                continue;
            if (statuses.length == 0)
                continue;
            for (int i = 0; i < statuses.length; i++) {
                if (statuses[i].hasData()) {
                    simsToExport.add(simulation);
                    continue;
                }
            }
        // String dbDriverName = PropertyLoader.getProperty(PropertyLoader.dbDriverName, null);
        // String dbConnectURL = PropertyLoader.getProperty(PropertyLoader.dbConnectURL, null);
        // String dbSchemaUser = PropertyLoader.getProperty(PropertyLoader.dbUserid, null);
        // String dbPassword = PropertyLoader.getSecretValue(PropertyLoader.dbPasswordValue, PropertyLoader.dbPasswordFile);
        // DataSetControllerImpl dsControllerImpl = new DataSetControllerImpl(null, new File(outputBaseDir), null);
        // 
        // code used to recover field data
        // 
        // HashMap<User, Vector<ExternalDataIdentifier>> allExternalDataIdentifiers = FieldDataDBOperationDriver.getAllExternalDataIdentifiers();
        // Enumeration<Variable> variables = simulation.getMathDescription().getVariables();
        // while(variables.hasMoreElements()) {
        // Variable var = variables.nextElement();
        // Expression exp = var.getExpression();
        // FieldFunctionArguments[] ffas = FieldUtilities.getFieldFunctionArguments( exp);
        // 
        // if(ffas != null && ffas.length > 0) {
        // FieldDataIdentifierSpec[] aaa = DataSetControllerImpl.getFieldDataIdentifierSpecs_private(
        // ffas, simulation.getVersion().getOwner(), true, allExternalDataIdentifiers);
        // 
        // System.out.println((ffas == null) ? "null" : exp.infix() + ", not null:" + ffas.length);
        // }
        // }
        }
    }
    if (outputBaseDir != null && bHasDataOnly == true && simsToExport.size() == 0) {
        CLIStandalone.writeSimErrorList(outputBaseDir, vcmlName + " has no simulations with any results.");
        for (String solverName : solverNames) {
            CLIStandalone.writeSimErrorList(outputBaseDir, "   " + solverName);
        }
        return false;
    }
    String rdfString = getMetadata(vcmlName, bioModel);
    XmlUtil.writeXMLStringToFile(rdfString, String.valueOf(Paths.get(outputDir, "metadata.rdf")), true);
    if (bMakeLogsOnly) {
        return false;
    }
    SEDMLExporter sedmlExporter = new SEDMLExporter(bioModel, sedmlLevel, sedmlVersion, simsToExport);
    String sedmlString = sedmlExporter.getSEDMLFile(outputDir, vcmlName, bForceVCML, bHasDataOnly, true);
    XmlUtil.writeXMLStringToFile(sedmlString, String.valueOf(Paths.get(outputDir, vcmlName + ".sedml")), true);
    // libCombine needs native lib
    ResourceUtil.setNativeLibraryDirectory();
    NativeLoader.load("combinej");
    boolean isDeleted = false;
    boolean isCreated;
    try {
        CombineArchive archive = new CombineArchive();
        String[] files;
        // TODO: try-catch if no files
        File dir = new File(outputDir);
        files = dir.list();
        for (String sd : files) {
            if (sd.endsWith(".sedml")) {
                archive.addFile(Paths.get(outputDir, sd).toString(), // target file name
                "./" + sd, KnownFormats.lookupFormat("sedml"), // mark file as master
                true);
            } else if (sd.endsWith(".sbml") || sd.endsWith(".xml")) {
                archive.addFile(Paths.get(outputDir, sd).toString(), "./" + sd, KnownFormats.lookupFormat("sbml"), // mark file as master
                false);
            } else if (sd.endsWith(".rdf")) {
                archive.addFile(Paths.get(outputDir, sd).toString(), "./" + sd, "http://identifiers.org/combine.specifications/omex-metadata", // KnownFormats.lookupFormat("xml"),
                false);
            }
        }
        archive.addFile(Paths.get(String.valueOf(vcmlFilePath)).toString(), "./" + vcmlName + ".vcml", "http://purl.org/NET/mediatypes/application/vcml+xml", false);
        // writing into combine archive
        String omexPath = Paths.get(outputDir, vcmlName + ".omex").toString();
        File omexFile = new File(omexPath);
        // Deleting file if already exists with same name
        if (omexFile.exists()) {
            omexFile.delete();
        }
        isCreated = archive.writeToFile(omexPath);
        // Removing all other files(like SEDML, XML, SBML) after archiving
        for (String sd : files) {
            // removing
            if (sd.endsWith(".sedml") || sd.endsWith(".sbml") || sd.endsWith("xml") || sd.endsWith("vcml") || sd.endsWith("rdf")) {
                isDeleted = Paths.get(outputDir, sd).toFile().delete();
            }
        }
        if (isDeleted)
            System.out.println("Removed intermediary files");
    } catch (Exception e) {
        throw new RuntimeException("createZipArchive threw exception: " + e.getMessage());
    }
    return isCreated;
}